Are you sure that wasn't The History Channel's "How The Earth Was Made" that you saw?
How the Earth Was Made
I watched most of it, but my DVR is acting up. I don't remember seeing anything about Jupiter.
I'm only a novice, but I don't think a shift in magnetic poles would send astroids flinging in all directions. The magnetosphere has nothing to do with gravity, mass and inertia which is what holds rocks, both large and small in their orbits. It has a lot to do with protecting life from cosmic rays, though.
The early solar system was an accretion disc, not unlike the one in this link.
Magnetic field of FU Orionis
There had to be lots of chaotic interaction over the millions of years during that period, it is quite probable that iron astroids would have struck the Earth by the thousands regardless of any interaction with Jupiter, but Jupiter may have played a role in any case.